TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv2985/mutT1:

update plot	correlation	link to info on gene
Rv0505c/serB1	(cc=0.4991)	info on Rv0505c/serB1
Rv1059/-	(cc=0.4928)	info on Rv1059/-
Rv1752/-	(cc=0.478)	info on Rv1752/-
Rv1505c/-	(cc=0.4747)	info on Rv1505c/-
Rv1806/PE20	(cc=0.4625)	info on Rv1806/PE20
Rv2160c/-	(cc=0.46)	info on Rv2160c/-
Rv1422/-	(cc=0.4477)	info on Rv1422/-
Rv2650c/-	(cc=0.4405)	info on Rv2650c/-
Rv1239c/corA	(cc=0.4376)	info on Rv1239c/corA
Rv2134c/-	(cc=0.4372)	info on Rv2134c/-

Correlation of Rv2985/mutT1 with Rv1505c/-

Normalized LFCs for Rv2985/mutT1:
(description and provenance of datasets)

	Rv2985/mutT1	Rv1505c/-
Fe_supp_jason_reseq	0.066	0.398
low_pH_jason_reseq	0.765	-0.35
NO_jason_reseq	0.221	0.247
B6_jason_reseq	-1.397	-1.795
MHCII_jason_reseq	-1.508	-1.356
Isoniazid02	0.876	1.695
Rifampicin4	-0.29	-0.244
Ethambutol3	0.122	0.896
Meropenem3	-0.34	-0.284
Vancomycin16	-0.069	0.0
Rv2680_day32	-0.83	-0.332
H37Rv_KO_MarP	0.419	-0.579
hypoxia_3wks	0.327	-0.144
hypoxia_6wks	0.282	0.0
glycerol	0.784	-0.396
cholesterol	-0.773	-0.847
AJ	-0.541	-0.071
Bibs02	-0.368	0.604
Bibs02c	0.444	-0.567
BL6	0.939	1.544
BL6a	0.907	1.908
BXD01	-0.143	1.315
BXD010	0.749	1.351
BXD011	0.583	1.424
BXD03	0.597	1.73
BXD04	0.34	1.686
BXD05	0.639	1.878
BXD06	0.677	2.076
BXD07	-0.074	1.562
BXD08	1.096	1.373
BXD09	0.356	2.422
CAST	0.853	0.709
CCcont	0.317	1.366
DS01	0.648	0.204
DS02	-0.978	-1.511
DS04	-1.211	0.641
DS0c	-0.116	-0.506
GP01	0.996	0.539
GP02	0.511	0.938
GP0c	1.231	0.511
NOD	0.0	2.294
NZO	0.701	-0.786
PWK	0.539	0.274
H37Rv_KO_CtpC	0.85	1.294
H37Rv_KO_CtpD	1.239	2.274
H37Rv_KO_Rv1272	0.669	1.29
H37Rv_KO_SugABC	0.623	-0.748
H37Rv_KO_MbtN	-0.31	1.363
Trans05	0.131	1.179
macrophage_unactivated	-0.303	0.167
IL1	0.641	0.489
Rapamycin	0.601	0.203
Tcell	-0.153	0.73
GMCSF	-0.671	-0.219
IFNab	-0.142	0.16
IFNg	-0.393	-0.072
IFNg_GMCSF1	-0.625	0.167
Rv1432_day32	-0.428	0.288
Rv1565c_day32	-0.13	-0.292
secA2_input	-1.016	-1.018
delta_Rv3594	1.366	0.197
delta_Rv3717	0.337	-0.56
delta_Rv3811	0.128	0.223
delta_Rv0954	1.154	0.656
PonA1	0.57	-0.164
EccD1_KO	0.204	0.059
EspI_KO	0.667	-0.163
PE35_KO	0.123	-0.055
PPE68_KO	-0.208	-0.368
glycerol2	-0.069	-0.488
lignocerate	-1.61	-0.477
oleate	-0.216	-0.432
phosphatidylcholine	-1.541	-0.098
acetate	0.155	-0.848
glucAc	-0.847	-1.106
Rv0950ko	-0.16	0.6
Rv1096ko	0.449	-0.525
Rv3684ko	0.0	0.311
delta_otsA_trehalose	-0.486	1.395